We have developed an integrated and multidisciplinary research program centralized around systems and computational biology. The latest systems and computational biology approaches have been exploited to address the research challenges in biofuel, biotechnology, and plant defense. Specifically, systems biology approaches have been employed to explore the natural biomass utilization systems for reverse design of biorefinery. We have been using the latest computational and experimental structure dynamics tools to engineer enzymes for better stability and compatibility. We have been using systems and computational biology to guide the redesigning pathways for various biomolecules for fuels and chemicals. In addition, different omics platforms were used to study plant defense against insects.